BACKGROUND: Serotonin is associated with symptoms of the irritable bowel syndrome, its action is terminated by the serotonin transporter protein. AIM: To assess the association between a functional polymorphism in the gene encoding for activity of the serotonin transporter protein and the irritable bowel syndrome. METHODS: Meta-analysis of studies identified through a Medline, PubMed and Web of Science search, describing the prevalence of a polymorphism in the serotonin transporter gene creating long and short alleles. RESULTS: Eight eligible studies described a total of 1034 patients with the irritable bowel syndrome, and 1377 healthy controls. Presence of the short allele is not associated with an increased risk for the irritable bowel syndrome: OR 1.0; 95% CI: 0.7-1.4 for homozygous subjects, and OR 1.0; 95% CI: 0.8-1.2 for homozygous subjects and heterozygotes together. Although Caucasians and Asians had diverging genotypic frequencies, no association with the shot allele and irritable bowel syndrome was observed in subgroups: Asians OR 1.2; 95% CI: 0.9-1.6 and OR 1.1; 95% CI: 0.2-5.9; Caucasians OR 0.9; 95% CI: 0.5-1.7 and OR 0.9; 95% CI: 0.7-1.2, respectively, for homozygous subjects alone and for homozygous subjects and heterozygotes together. CONCLUSION: A genetic polymorphism in the gene encoding for activity of the serotonin transporter protein is not associated with the irritable bowel.